NEWS

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coloc 5.2.3 (2023-10-03)

• minor change, for another package to be able to access one of the internal functions, it was exported

coloc 5.2.2 (2023-05-12)

• better checking of dataset inputs, and better documentation of what that data should look like

coloc 5.2.0

• update to new susieR >= 0.12.06 which requires sample size
• general tidy up of susie-related code
• new functions to help find subregions for finemapping - findpeaks, findends
• updated FAQ.md
• tidied empty items in documentation to make CRAN happy
• slimmed down example dataset to make CRAN even happier

coloc 5.1.2

• deprecate runsusie() argument p

coloc 5.1.1

• update plot_dataset() and sensitivity() to fix bug for very small p values displaying as 0

coloc 5.1.0 (2021-06-14)

• release to CRAN of coloc.susie
• remove nref now not recommended

coloc 5.0.0.9002

• in runsusie, allow nref to be overridden if user passes z_ld_weight

coloc 5.0.0.9001

• deprecate coloc.signals for multiple causal variants
• introduce coloc.susie for multiple causal variants
• new vignette 02_data giving more details on structuring your data properly

coloc 4.0-5

• update error checking

coloc 4.0-3

• BUGFIX

• missing sdY for type="quant" would error in finemap.signals or coloc.signals, now it is estimated if missing.
• warning for factors used as snp names added (issue #29)

coloc 4.0-2

• BUGFIX

• snps in the second dataset might not have been masked as intended. This would result in effect using the "single" option for trait 2 when masking was expected.

coloc 4.0-0

new functions: coloc.signals, finemap.abf

• analogues of coloc.abf and finemap.abf that allow for multiple causal variants. See vignette on conditioning/masking new function: sensitivity
• post-hoc, determine the sensitivity of coloc results to changes in the prior. See vignette on sensitivity

2019-06-25

coloc 3.2-1 (2019-05-17)

• BUGFIX: finemap.abf()

• in low power situations, the posterior for H0 was previously too low. This will only affect datasets where the minimum p value was > 1e-7 - ie where the posterior for H0 would be expected to be much above 0.

coloc 3.2

• fix bug in process.datasets which suggested MAF was needed for cc data when beta/varbeta also present
• added pkgdown

2018-09-28

coloc 3.1 (2018-02-24)

new function: finemap.abf

• improved clarity of error messages in coloc.abf() sub functions
• added finemap.abf to fine map a single trait
• fixed warnings caused by CRAN disliking the BioConductor devel branch

2018-02-22

coloc 2.4

• added stratification to proportional testing approaches

2017-03-21

coloc 2.3-2

• tidied code relating mainly to proportional
• colocalisation testing methods, making more methods confirm to S4.
• pcs.prepare now imputes missing genotypes by default 2013-05-22

coloc 2.3 (2013-09-25)

coloc BUGFIX

• Introduced a function to estimate trait variance from supplied coefficients and standard errors. This is used within the approach implemented in coloc.abf(), and replaces the earlier version which implicitly assumed that var(Y)=1 for quantitative traits, which could lead to incorrect inference when var(Y) was far from 1.

2013-09-25

coloc 2.2 (2013-06-19)

• Merged coloc.abf and coloc.abf.imputed(), so that datasets for which beta, var(beta) are available can be matched to datasets with only p values and maf.2 This means the arguments to coloc.abf() have been changed! Please check ?coloc.abf for the new function.

2013-19-06

coloc 2.1 (2013-06-03)

• Bug fix for coloc.abf() function, which used p12 instead of log(p12) to calculate L4.
• New function coloc.abf.imputed() to make better use of fuller information on imputed data.

2013-03-06

coloc 2.0 (2013-05-23)

• New function, coloc.abf(), to implement the colocalisation approach described by Giambartolomei et. al.
• Changes in the coloc.test() and coloc.bma() functions to make them consistent with regards arguments and output.

2013-22-05

coloc 1.11 (2013-01-25)

• added principal components functions pcs.prepare(), pcs.model().
• Restructed the coloc objects to separate Bayesian and non-Bayesian inference.

2012-12-10

coloc 1.10 (2012-11-30)

• added Credible Interval calculation to coloc.test().

2012-11-28

coloc 1.09

• updated to return u and Var(u) in addition to chisq statistic.

2012-07-12

coloc 1.08 (2012-04-12)

• fixed error in documentation, added MASS to Depends.

2012-04-12

coloc 1.06

• some tidying.

2012-01-05

coloc 1.05 (2012-01-04)

• moved to S4 methods.

2012-01-03

coloc 1.04

• made the means of generating plots more flexible.

2011-12-27